Abstract: The widely used BEPU method is to quantify the important uncertain source (input uncertainty) associated with the power plant and models, and then propagate the uncertainty to obtain the double 95% uncertainty bands of the safety related parameters (such as the peak cladding temperature, PCT). However, as the important sources of uncertainty, some physical model parameters in the best estimation (BE) codes are often difficult to be directly measured in the experiments. The quantification process is mainly dependent on the expert judgment which lacks objectivity. In this paper, based on the Expectation Maximization (EM) algorithm and the response parameters measured directly from the separate effect test, the probability density distribution of the internal model parameters can be derived by solving the inverse problem. Then, the application of the method is performed by taking reflood phenomena as an example. Uncertainties of code internal boiling heat transfer and interfacial friction models are obtained.